In THcAerogel.cxx, mean pedestals are calculated if
	fMinPeds>0. Set fMinPeds to default zero in
	THcAerogel::InitializePedestals. Reinitialize it with
	paero_min_peds parameter in paero.param file.

Modify THcDC::CoarseTrack and THcDC::TrackFit

Add variables fX_fp_best,fY_fp_best,fXp_fp_best,fYp_fp_best to THcDC.h
Modified THcDC::CoarseTrack so that the variables are filled with the
quantities from the track with the smallest chi-squared.
Modified THcDC::TrackFit so that the fResidual per plane is filled with
for the track with the lowest chi-squared.
Modified THcDC::DefineVariables so that access the variables as
dc.x_fp,dc.y_fp,dc.xp_fp and dc.yp_fp

Modified THcCherenkov.cxx and THcCherenkov.h

Add array fADC_hit that is a flag if there is a hit in the ADC
fADC_hit is set in Decode method
The FADC has a threshold on accepting ADC hit
Modified CoarseProcess method to eliminate old FASTBUS bias in the analysis

Modify ShowerPlane and ShowerArray ProcessHits Methods

Remove the hc_hodo_calib directory

The hc_hodo_calib directory is now under hallc_replay/CALIBRATION

Modified hodoscope and scintillatorplane code for hodo calibration

Temporarily set THcHodoscope.cxx so that only the first three planes are used to calculate the focal
plane time and beta.
In THcHodoscope , Modified format for writing out the dump file used in hodo calibration.
Add cosmicflag to THcScintillatorPLane so the corrected time is done right for cosmics.
Modified hc_hodo_calib/tofcal.f so that it uses detector 10 as the reference
and that it writes out better defualts for parameters in there are not enough events for a PMT.

Modify THcHodoHit.h and THcScintillatorPlane.cxx

THcHodoHit.h add methods to set and get the ADC peak amp and time
THcScintillatorPlane::ProcessHits changed to set the ADC peak amp and time in the Hodohit
DefineVariable added variables to tree

   Used by hodtest.C example (for old HMS data)

Modified THcHodoscope::FineProcess for dumping data for hodo calibrations

Moved the writing out of the "0" to the fDumpOut for hodo calibrations
to immediatiately after the TOF with track info calculations.
Before it had been after then lines

  if ( !fChern || !fShower ) {
    return 0;
  }

so if Cerenkov and shower were not used in replay the code would not get
to write out the "0" which is used to denote the end of an event data for
the calibration script.

Added capability to set F250 parameters from PSE125.

PSE125 holds information about setting of F250 modules. Now this
information is used to set `fNPedestalSamples` and `fNPeakSamples`
parameters of `THcRawAdcHit`.

This is done through `THcHitList`, since it has information about
which crate and module each channel is in. Currently, the information
is set for each event, because of the hitlist and analyzer design.

I added the neccessary support for these changes to all raw hit
classes.

  Provides methods get NSA, NSB, and NPED for each crate

Corrected warning message for missing refchan to correctly display reference channel.
Modified warningg message for missing refindex to include information about reference channel.

	Cycle over array of pedestal subtracted fADC signals fA_p in
	the same order as it was filled.

fScinHitPaddle is a std::vector<std::vector<Double_t>>. It was
cleared and rebuilt for each event with the same structure,
instead of just zeroing out all the values.

Now it is created in only one place, and than zeroed instead of
cleared.

Changed data type in fScinHitPaddle from Double_t to Int_t. Should
be changed to bool, but then all logic should be changed.

There was a weird bug in the code, that only triggered for some runs.
It turns out, in the `THcHodoscope::FineProcess` the hits in each plane
were created only for number of paddles in first plane. SHMS, however,
has 13 paddles in first plane and 14 and 21 paddles in last two planes.

The problem is fixed now, but part of that code should be rewritten for
efficiency.

Eliminate variables from THcScintillatorPlane::DefineVariables

With the new raw and good varibles added to the tree, these variables are not needed in the tree.

Applied changes in several files to reflect this.
Minor fix in `THcRawHodoHit`.

Pooser hms dc residual work

When calculating the residuals, consider all track candidates instead of only the first track.  Moreover, eliminate the instances when there was no hit in a plane then the residual was returned as zero.

This error is triggered when there is no wire defined for hit, or
when the wire has no `GetTDDConv()` method. The ROOT dictionary
calls default constructor that doesn't set the wire and calls
`ConvertTimeToDist()` regardless.

I changed the default constructor to not call the `ConvertTimeToDist()`
if the wire is not set. I also added the call to this function
in the `SetWire()` method.

Add fCosmicFlag to Hodoscope class

The fCosmicFlag is used in EstimateFocalPlaneTime
The start time for the drift chamber is determined as an average
of the focal plane times for each hodo plane. Need to account for
the TOF from the hodoscope to the focal plane (z=0). For cosmic
data need to add this TOF to the corrected scintillator time, while
usually one needs to subtract this TOF. Add a flag as parameter to
switch between these modes.

`THcTrigRawHit` now uses raw ADC and TDC classes.
Added new leaves to the `THcTrigDet` Root output.